erator-activated receptor type gamma (PPAR␥) is a subgroup of the PPAR transcription factor family. Recent studies indicate that loss of PPAR␥ is associated with the development of pulmonary hypertension (PH). We hypothesized that the endothelial dysfunction associated with PPAR␥ inhibition may play an important role in the disease process by altering cellular gene expression and signaling cascades. We utilized microarray analysis to determine if PPAR␥ inhibition induced changes in gene expression in pulmonary arterial endothelial cells (PAEC). We identified 100 genes and expressed sequence tags (ESTs) that were upregulated by Ͼ1.5-fold and 21 genes and ESTs that were downregulated by Ͼ1.3-fold (P Ͻ 0.05) by PPAR␥ inhibition. The upregulated genes can be broadly classified into four functional groups: cell cycle, angiogenesis, ubiquitin system, and zinc finger proteins. The genes with the highest fold change in expression: hyaluronan-mediated motility receptor (HMMR), VEGF receptor 2 (Flk-1), endothelial PAS domain protein 1 (EPAS1), basic fibroblast growth factor (FGF-2), and caveolin-1 in PAEC were validated by real time RT-PCR. We further validated the upregulation of HMMR, Flk-1, FGF2, and caveolin-1 by Western blot analysis. In keeping with the microarray results, PPAR␥ inhibition led to re-entry of cell cycle at G1/S phase and cyclin C upregulation. PPAR␥ inhibition also exacerbated VEGF-induced endothelial barrier disruption. Finally we confirmed the downregulation of PPAR␥ and the upregulation of HMMR, Flk-1, FGF2, and Cav-1 proteins in the peripheral lung tissues of an ovine model of PH. In conclusion, we have identified an array of endothelial genes modulated by attenuated PPAR␥ signaling that may play important roles in the development of PH. microarray; cell signaling; peroxisome proliferator-activated receptor PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-␥ (PPAR␥) was initially identified in adipose tissue and is a key regulator of lipid metabolism and glucose homeostasis (47, 50). Later, it was shown that PPAR␥ is also expressed in the vasculature including endothelial cells (ECs), vascular smooth muscle cells (VSMCs), and monocytes/macrophages (13, 43). Upon activation by its ligands (fatty acids, arachidonic acid metabolites, and thiazolidinediones, etc), PPAR␥ forms heterodimers with the retinoid X receptor (RXR), and binds to specific PPAR response elements (PPRE) in the promoter region of its target genes, thereby regulating downstream gene expression (15,46). PPAR␥-mediated gene regulation can also be modulated by its interactions with specific co-activators and co-repressors (15, 26). PPAR␥ activation has been shown to alleviate atherosclerotic lesion formation and tumor progression (25, 30). The antiproliferative effects on VSMCs and antiangiogenic effects on tumor vasculogenesis by PPAR␥ activation seem to play important roles in these beneficial effects (9,31,53).Recently, it has been shown that loss of PPAR␥ is associated with pulmonary hypertension (PH) (35). PPAR␥ expression has been sho...